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Behairy MY, Eid RA, Otifi HM, Mohammed HM, Alshehri MA, Asiri A, Aldehri M, Zaki MSA, Darwish KM, Elhady SS, El-Shaer NH, Eldeen MA. Unraveling Extremely Damaging IRAK4 Variants and Their Potential Implications for IRAK4 Inhibitor Efficacy. J Pers Med 2023; 13:1648. [PMID: 38138875 PMCID: PMC10744719 DOI: 10.3390/jpm13121648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/24/2023] Open
Abstract
Interleukin-1-receptor-associated kinase 4 (IRAK4) possesses a crucial function in the toll-like receptor (TLR) signaling pathway, and the dysfunction of this molecule could lead to various infectious and immune-related diseases in addition to cancers. IRAK4 genetic variants have been linked to various types of diseases. Therefore, we conducted a comprehensive analysis to recognize the missense variants with the most damaging impacts on IRAK4 with the employment of diverse bioinformatics tools to study single-nucleotide polymorphisms' effects on function, stability, secondary structures, and 3D structure. The residues' location on the protein domain and their conservation status were investigated as well. Moreover, docking tools along with structural biology were engaged in analyzing the SNPs' effects on one of the developed IRAK4 inhibitors. By analyzing IRAK4 gene SNPs, the analysis distinguished ten variants as the most detrimental missense variants. All variants were situated in highly conserved positions on an important protein domain. L318S and L318F mutations were linked to changes in IRAK4 secondary structures. Eight SNPs were revealed to have a decreasing effect on the stability of IRAK4 via both I-Mutant 2.0 and Mu-Pro tools, while Mu-Pro tool identified a decreasing effect for the G198E SNP. In addition, detrimental effects on the 3D structure of IRAK4 were also discovered for the selected variants. Molecular modeling studies highlighted the detrimental impact of these identified SNP mutant residues on the druggability of the IRAK4 ATP-binding site towards the known target inhibitor, HG-12-6, as compared to the native protein. The loss of important ligand residue-wise contacts, altered protein global flexibility, increased steric clashes, and even electronic penalties at the ligand-binding site interfaces were all suggested to be associated with SNP models for hampering the HG-12-6 affinity towards IRAK4 target protein. This given model lays the foundation for the better prediction of various disorders relevant to IRAK4 malfunction and sheds light on the impact of deleterious IRAK4 variants on IRAK4 inhibitor efficacy.
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Affiliation(s)
- Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt;
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (R.A.E.); (H.M.O.)
| | - Hassan M. Otifi
- Department of Pathology, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (R.A.E.); (H.M.O.)
| | - Heitham M. Mohammed
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Mohammed A. Alshehri
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia; (M.A.A.)
| | - Ashwag Asiri
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia; (M.A.A.)
| | - Majed Aldehri
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Mohamed Samir A. Zaki
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Nahla H. El-Shaer
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig 44511, Egypt;
| | - Muhammad Alaa Eldeen
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig 44511, Egypt;
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Erguven M, Kilic S, Karaca E, Diril MK. Genetic complementation screening and molecular docking give new insight on phosphorylation-dependent Mastl kinase activation. J Biomol Struct Dyn 2023; 41:8241-8253. [PMID: 36270968 DOI: 10.1080/07391102.2022.2131627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/26/2022] [Indexed: 10/24/2022]
Abstract
Mastl is a mitotic kinase that is essential for error-free chromosome segregation. It is an atypical member of AGC kinase family, possessing a unique non-conserved middle region. The mechanism of Mastl activation has been studied extensively in vitro. Phosphorylation of several residues were identified to be crucial for activation. These sites correspond to T193 and T206 in the activation loop and S861 in the C-terminal tail of mouse Mastl. To date, the significance of these phosphosites was not confirmed in intact mammalian cells. Here, we utilize a genetic complementation approach to determine the essentials of mammalian Mastl kinase activation. We used tamoxifen-inducible conditional knockout mouse embryonic fibroblasts to delete endogenous Mastl and screened various mutants for their ability to complement its loss. S861A mutant was able to complement endogenous Mastl loss. In parallel, we performed computational molecular docking studies to evaluate the significance of this residue for kinase activation. Our in-depth sequence and structure analysis revealed that Mastl pS861 does not belong to a conformational state, where the phosphoresidue contributes to C-tail docking. C-tail of Mastl is relatively short and it lacks a hydrophobic (HF) motif that would otherwise help its anchoring over N-lobe, required for the final steps of kinase activation. Our results show that phosphorylation of Mastl C-tail turn motif (S861) is dispensable for kinase function in cellulo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mehmet Erguven
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Seval Kilic
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - M Kasim Diril
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
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Bello M, Bandala C. Evaluating the ability of end-point methods to predict the binding affinity tendency of protein kinase inhibitors. RSC Adv 2023; 13:25118-25128. [PMID: 37614784 PMCID: PMC10443623 DOI: 10.1039/d3ra04916g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
Because of the high economic cost of exploring the experimental impact of mutations occurring in kinase proteins, computational approaches have been employed as alternative methods for evaluating the structural and energetic aspects of kinase mutations. Among the main computational methods used to explore the affinity linked to kinase mutations are docking procedures and molecular dynamics (MD) simulations combined with end-point methods or alchemical methods. Although it is known that end-point methods are not able to reproduce experimental binding free energy (ΔG) values, it is also true that they are able to discriminate between a better or a worse ligand through the estimation of ΔG. In this contribution, we selected ten wild-type and mutant cocrystallized EGFR-inhibitor complexes containing experimental binding affinities to evaluate whether MMGBSA or MMPBSA approaches can predict the differences in affinity between the wild type and mutants forming a complex with a similar inhibitor. Our results show that a long MD simulation (the last 50 ns of a 100 ns-long MD simulation) using the MMGBSA method without considering the entropic components reproduced the experimental affinity tendency with a Pearson correlation coefficient of 0.779 and an R2 value of 0.606. On the other hand, the correlation between theoretical and experimental ΔΔG values indicates that the MMGBSA and MMPBSA methods are helpful for obtaining a good correlation using a short rather than a long simulation period.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Diaz Mirón s/n, Col. Casco de Santo Tomas Ciudad de México 11340 Mexico
| | - Cindy Bandala
- Escuela Superior de Medicina, Instituto Politécnico Nacional México City 11340 Mexico
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Erguven M, Cornelissen NV, Peters A, Karaca E, Rentmeister A. Enzymatic Generation of Double-Modified AdoMet Analogues and Their Application in Cascade Reactions with Different Methyltransferases. Chembiochem 2022; 23:e202200511. [PMID: 36288101 PMCID: PMC10100234 DOI: 10.1002/cbic.202200511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/26/2022] [Indexed: 01/25/2023]
Abstract
Methyltransferases (MTases) have become an important tool for site-specific alkylation and biomolecular labelling. In biocatalytic cascades with methionine adenosyltransferases (MATs), transfer of functional moieties has been realized starting from methionine analogues and ATP. However, the widespread use of S-adenosyl-l-methionine (AdoMet) and the abundance of MTases accepting sulfonium centre modifications limit selective modification in mixtures. AdoMet analogues with additional modifications at the nucleoside moiety bear potential for acceptance by specific MTases. Here, we explored the generation of double-modified AdoMets by an engineered Methanocaldococcus jannaschii MAT (PC-MjMAT), using 19 ATP analogues in combination with two methionine analogues. This substrate screening was extended to cascade reactions and to MTase competition assays. Our results show that MTase targeting selectivity can be improved by using bulky substituents at the N6 of adenine. The facile access to >10 new AdoMet analogues provides the groundwork for developing MAT-MTase cascades for orthogonal biomolecular labelling.
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Affiliation(s)
- Mehmet Erguven
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
- Cells in Motion Interfaculty CentreUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
| | - Nicolas V. Cornelissen
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
| | - Aileen Peters
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center35330IzmirTurkey
- Izmir International Biomedicine and Genome InstituteDokuz Eylul University, 35340 Izmir (Turkey)
| | - Andrea Rentmeister
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
- Cells in Motion Interfaculty CentreUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
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